Below, Sports Mole takes a closer look at the key talking points from the game.
On target: 5
On target: 12
Was the result fair?
There was certainly no disputing that Bayern did enough to collect all three points in a game which counted for very little in Croatia. Despite making plenty of changes, Guardiola's side always looked sharper in possession and they showed more attacking intent from the first whistle. Dinamo did enjoy spells on top, but their lack of quality in attack proved to be vital as they struggled to make the most of opportunities on the break. It was not a classic Bayern display, but with so many world-class players in the side, the visitors always looked likely to pull away from Dinamo.
Dinamo Zagreb's performance
Zoran Mamic knew that the damage had been done before this game, with Dinamo already forced to accept that they would finish bottom of Group F. In truth, this was one of the better displays as they defended well as a unit for long spells. It was clear that Mamic wanted his side to hit the visitors on the break, and their shape was impressive in the first half as they remained narrow in midfield to ensure they were difficult to break down.
The statistics show that Bayern dominated for much of the evening, but Dinamo will feel that an opportunity may have been missed. El Arbi Hillel Soudani wasted two great chances before the break, and had either been taken, Dinamo could have hit Bayern on the break even more frequently. As soon as they fell behind, the game was over. The hosts simply did not have the quality in attack to trouble Bayern and they paid the price.
Bayern Munich's performance
Guardiola took the opportunity to start a number of players on the fringe of the side, and he will be pleased to see those individuals produce impressive performances. It will not be remembered as a classic Bayern display, but they retained the control for much of the night with their patient approach to the game. Philipp Lahm and Xabi Alonso dictated the tempo for long spells as the visitors searched for openings, while Sebastian Rode certainly took his chance with an energetic display in the centre of midfield.
It was the introduction of Muller at the break that changed the game as his running off the ball and eagerness to step up the tempo put more pressure on the Dinamo defence. With Lewandowski in the side, goals seem almost inevitable and he took his two best chances to hand Bayern the control. Could Bayern have played better? Yes, they did not always show the cutting edge we are used to seeing in attacking areas. However, it is difficult to be too critical after they entered the match having already won the group. Muller missed the chance to add gloss to the scoreline late on, but this was a routine win for Guardiola's men.
Sports Mole's man of the match
Xabi Alonso: Muller pushed the Spaniard hard for this after making such a big impact, but Alonso just beats his teammate to the honour. It was a trademark Alonso display as he moved the ball efficiently and started attacks with some excellent passes from a deep position. Bayern had to remain patient and he was key to keeping the pressure on the hosts.
Muller was excellent after coming off the bench, but his decision to take the penalty rather than give Lewandowski the chance to complete his hat-trick ended in frustration as he sent his effort against the post. His teammate might be having a few jokes with him on the flight home.
Martin Stromberggson completed his shift without much fuss and he was certainly right to point to the spot after Eduardo had made contact with Arturo Vidal in the box. A good display from the referee.
Dinamo Zagreb: Mamic's side make the trip to Osijek on Sunday afternoon.
Bayern: After suffering their first Bundesliga defeat of the season last weekend, Bayern return to league action with a home fixture against FC Ingolstadt 04 on Saturday.